Tag: pubmed

J Comput Biol. 2022 May 20. doi: 10.1089/cmb.2021.0536. Online ahead of print.

ABSTRACT

The comparison of DNA sequences is of great significance in genomics analysis. Although the traditional multiple sequence alignment (MSA) method is popularly used for evolutionary analysis, optimally aligning k sequences becomes computationally intractable when k increases due to the intrinsic computational complexity of MSA. Despite numerous k-mer alignment-free methods being proposed, the existing k-mer alignment-free methods may not truly capture the contextual structures of the sequences. In this study, we present a novel k-mer contextual alignment-free method (called kmer2vec), in which the sequence k-mers are semantically embedded to word2vec vectors, an essential technique in natural language processing. Consequently, the method converts each DNA/RNA sequence into a point in the word2vec high-dimensional space and compares DNA sequences in the space. Because the word2vec vectors are trained from the contextual relationship of k-mers in the genomes, the method may extract valuable structural information from the sequences and reflect the relationship among them properly. The proposed method is optimized on the parameters from word2vec training and verified in the phylogenetic analysis of large whole genomes, including coronavirus and bacterial genomes. The results demonstrate the effectiveness of the method on phylogenetic tree construction and species clustering. The method running speed is much faster than that of the MSA method, especially the phylogenetic relationships constructed by the kmer2vec method are more accurate than the conventional k-mer alignment-free method. Therefore, this approach can provide new perspectives for phylogeny and evolution and make it possible to analyze large genomes. In addition, we discuss special parameterization in the k-mer word2vec embedding construction. An effective tool for rapid SARS-CoV-2 typing can also be derived when combining kmer2vec with clustering methods.

PMID:35593919 | DOI:10.1089/cmb.2021.0536

Biomed Phys Eng Express. 2022 May 19. doi: 10.1088/2057-1976/ac7169. Online ahead of print.

ABSTRACT

Objective:To estimate organs’ absorbed dose from the two-phase CT of parathyroid glands, effective dose (ED) based on three different methods, and compare the dose values with those reported by other published protocols.Methods:Volumetric-computed-tomography-dose-index (CTDIvol), dose-length-product (DLP), and the corresponding scan length during each phase of a parathyroid protocol were recorded, for seventy-six patients. One k-factor, and two different k-factors for the neck and chest area were used to estimate the ED from DLP. A Monte Carlo software, VirtualDoseCT, was also used for the estimation of organs’ absorbed dose and ED.Results:Two-phase parathyroid CT resulted in a mean ED of 3.93 mSv, 4.29 mSv and 4.21 mSv according to the one k-factor, two k-factors, and VirtualDoseCT methods, respectively. The two k-factors method resulted in a slight overestimation of 1.9% in total ED compared to VirtualDoseCT. No statistically significant difference was found in ED values between these methods (Wilcoxon test, p>0.05), except for female patients in the pre-contrast phase. The organs inside the SFOV received the following doses: thymus 23.3 mGy, lungs 11.5 mGy, oesophagus 9.2 mGy, thyroid 6.9 mGy, and breast 6.3 mGy. The ED and organs’ dose (OD) values were significantly lower in the pre-contrast than in the arterial phase (Wilcoxon test, p<0.001). A statistically significant difference was observed between male and female patients for the pre-contrast phase (Mann-Whitney test, p<0.05), regarding the ED values obtained with the two k-factors method and VirtualDoseCT software.Conclusions:The two k-factors method could be applied for the ED estimation in clinical practice, if appropriate software is not available. An extensive range of ED values derived from the literature, mainly depending on the acquisition protocol parameters and the estimation method.

PMID:35593909 | DOI:10.1088/2057-1976/ac7169

Mol Biol Rep. 2022 May 20. doi: 10.1007/s11033-022-07563-2. Online ahead of print.

ABSTRACT

BACKGROUND: Diagnostic and prognostic significance of epithelial-to-mesenchymal transition (EMT) associated biomarkers are evaluated in a cohort of NMIBC (non-muscle invasive bladder cancer) and MIBC (muscle invasive bladder cancer) patients.

METHODS AND RESULTS: Real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining were carried out in 100 tumor specimens (59 NMIBC and 41 MIBC). The expressions of the epithelial marker, mesenchymal markers and EMT-activating transcription factors (EMT-ATFs) were determined at transcriptome and protein level followed by their statistical associations with clinicohistopathological variables of the patients. Transcriptomic expression analysis showed statistical relevance of tumor stage with increased Twist and Zeb-1; tumor type with reduced E-cadherin and increased Snail; and smoking/tobacco chewing status (S/TC) of patients with increased N-cadherin and Snail in NMIBC patients. Tumor grade with reduced message E-cadherin, gain of N-cadherin, Snail, Twist and Zeb-1; patients’ age with reduced E-cadherin and Twist gain; and tumor type with increased message N-cadherin exhibited associations in MIBC patients. Protein expression analysis identified statistical relevance of tumor grade with nuclear gain of Snail and Twist; and nuclear gain of Slug with S/TC status of NMIBC patients. Novel gain of membranous Vimentin deduced association with patients’ age in MIBC patients. Survival analysis identified novel Vimentin as the positive predictor of short progression free survival (PFS) and short overall survival (OS) in MIBC patients. Study established altered EMT profile as the independent negative predictor of short recurrence free survival (RFS) in NMIBC patients and positive predictor of short PFS and OS in MIBC patients.

CONCLUSIONS: EMT associated biomarkers could provide diagnostic and prognostic risk stratification and hence could be of importance in the clinical management of bladder cancer patients.

PMID:35593896 | DOI:10.1007/s11033-022-07563-2

Vascular. 2022 May 20:17085381221100380. doi: 10.1177/17085381221100380. Online ahead of print.

ABSTRACT

INTRODUCTION: This study aims to assess prevalence and prognostic implications of pre-existing peripheral artery disease (PAD) in patients infected by the SARS-CoV-2 by means of a systematic review and meta-analysis.

MATERIAL AND METHODS: We searched MEDLINE and Scopus to locate all the articles published up to 10 December 2021, reporting data on pre-existing PAD among COVID-19 survivors (S) and non survivors (NS). The pooled prevalence of pre-existing PAD in COVID-19 patients was calculated using a random effects model and presenting the related 95% confidence interval (CI), while the mortality risk was estimated using the Mantel-Haenszel random effects models with odds ratio (OR) and related 95% CI. Statistical heterogeneity was measured using the Higgins I² statistic.

RESULTS: Eight investigations, enrolling 13,776 COVID-19 patients (mean age: 67.1 years, 3.863 males), met the inclusion criteria and were included in the final analysis. The pooled prevalence of pre-existing PAD was 5.7% of cases (95% CI: 3.8-8.4%, p < 0.0001), with high heterogeneity (I² = 84.5%), which was directly correlated with age (p < 0.0001), previous hypertension (p = 0.003), and dyslipidaemia (p = 0.02) as demonstrated by the meta-regression. Moreover, pre-existing PAD was significantly associated with higher risk of short-term death in patients with SARS-CoV-2 infection (OR: 2.78, 95% CI: 2.37-3.27, p < 0.0001 I² = 0%); the sensitivity analysis confirmed yielded results.

CONCLUSIONS: Pre-existing PAD represents a comorbidity in about 1 out of 6 COVID-19 patients, but it is associated with a twofold higher risk of short-term mortality.

PMID:35593210 | DOI:10.1177/17085381221100380

Int Health. 2022 May 19:ihac030. doi: 10.1093/inthealth/ihac030. Online ahead of print.

ABSTRACT

BACKGROUND: Child marriage among women has become a major threat to the rights of women, especially in low- and middle-income countries. The marriage of girls below age 18 y is a major public and global health challenge. Therefore, this study examined the spatial pattern and factors associated with child marriage in Nigeria.

METHODS: The data were sourced from the 2018 Nigeria Demographic and Health Survey. The study included a total of 4283 young women aged 20-24 y. The findings were provided in the form of spatial maps and adjusted ORs (aORs) with 95% confidence interval (CI).

RESULTS: Hotspot areas for child marriage in Nigeria were located in Sokoto, Kebbi, Katsina, Kano, Jigawa, Yobe, Bauchi, Niger, Borno, Gombe, and Adamawa. The prevalence of child marriage in Nigeria was 41.50%. The likelihood of child marriage in Nigeria was high among those currently working (aOR=1.31; 95% CI 1.11 to 1.55) compared with young women who were not working. On the other hand, young women whose partners had secondary education and above (aOR=0.57; 95% CI 0.45 to 0.73) were less likely to report child marriage in Nigeria compared with those whose partners had no education.

CONCLUSIONS: The findings of the study indicate that there are several hotspots in Nigeria that need to be targeted when implementing interventions aimed at eliminating child marriage in the country.

PMID:35593176 | DOI:10.1093/inthealth/ihac030

Euro Surveill. 2022 May;27(20). doi: 10.2807/1560-7917.ES.2022.27.20.2100377.

ABSTRACT

BackgroundThe emergence of the SARS-CoV-2 Alpha variant in England coincided with a rapid increase in the number of PCR-confirmed COVID-19 cases in areas where the variant was concentrated.AimOur aim was to assess whether infection with Alpha was associated with more severe clinical outcomes than the wild type.MethodsLaboratory-confirmed infections with genomically sequenced SARS-CoV-2 Alpha and wild type between October and December 2020 were linked to routine healthcare and surveillance datasets. We conducted two statistical analyses to compare the risk of hospital admission and death within 28 days of testing between Alpha and wild-type infections: a matched cohort study and an adjusted Cox proportional hazards model. We assessed differences in disease severity by comparing hospital admission and mortality, including length of hospitalisation and time to death.ResultsOf 63,609 COVID-19 cases sequenced in England between October and December 2020, 6,038 had the Alpha variant. In the matched cohort analysis, we matched 2,821 cases with Alpha to 2,821 to cases with wild type. In the time-to-event analysis, we observed a 34% increased risk in hospitalisation associated with Alpha compared with wild type, but no significant difference in the risk of mortality.ConclusionWe found evidence of increased risk of hospitalisation after adjusting for key confounders, suggesting increased infection severity associated with the Alpha variant. Rapid assessments of the relative morbidity in terms of clinical outcomes and mortality associated with emerging SARS-CoV-2 variants compared with dominant variants are required to assess overall impact of SARS-CoV-2 mutations.

PMID:35593163 | DOI:10.2807/1560-7917.ES.2022.27.20.2100377

Expert Rev Cardiovasc Ther. 2022 May 20. doi: 10.1080/14779072.2022.2080055. Online ahead of print.

ABSTRACT

OBJECTIVES: Spontaneous coronary artery dissection (SCAD) may contribute to 35% of acute coronary syndrome among women ≤50 years of age. We aimed to investigate the overall incidence, as well as the trends of SCAD incidence based on race, household income, and the U.S. census regions utilizing the National Inpatient Sample.

METHODS: This is a retrospective cohort study, where discharge data were extracted from the NIS using 9th and 10th revisions of the International Classification Disease for SCAD.

RESULTS: : We found that the incidence of SCAD is rising, and patients were predominantly females. Crude incidence of SCAD per 1,000,000 discharges per year was found to be 4.95 (2010), 5.73 (2011), 5.34 (2012), 6.18 (2013), 7.64 (2014), 8.11 (2015), 14.58 (2016), and 14.81 (2017). Statistically significant differences were observed in year-to-year SCAD incidence among racial groups, household income quintiles, and U.S. census regions (P<0.0001).

CONCLUSION: : Recent trends (2017) indicate the highest incidence is among the White race, highest household income quintile, and in Census Region 4. These findings defy racial trends in cardiovascular disease burden which need further discovery.

PMID:35593175 | DOI:10.1080/14779072.2022.2080055

Biodemography Soc Biol. 2022 May 20:1-17. doi: 10.1080/19485565.2022.2072269. Online ahead of print.

ABSTRACT

This study is conducted to decompose inequality in four important micronutrient intakes, i.e. calcium, iodine, iron, and zinc due to socioeconomic factors during 2006-2016. For this purpose, data were taken from national-level surveys, i.e. HIES-2006 and HIICS-2016. We applied a recently proposed decomposition method based on copula function to decompose between year changes in the consumption of micronutrients into structure and composition effect. The results show that average calcium and iron intakes increased by 518.54 (mg) and 0.962 (mg), respectively, while average iodine and zinc intakes decreased by 2.009 (mg) and 3.411 (mg), respectively, during the decade. Estimates of structure effect show that calcium, iodine, and iron consumption increased on average, i.e. 525.316 (mg), 14.615 (mg), and 2.15 (mg), respectively, while zinc intake decreased by 2.735 (mg). The composition effect is negative for all the four micronutrients, implying that consumption of calcium, iodine, iron, and zinc decreased as 6.7766 (mg), 16.624 (mg), 1.189 (mg), and 0.677 (mg), respectively. The main factors of this change are household income, urbanization, provinces, and household size. The policymakers need to know the importance of socioeconomic factors to improve hidden hunger in terms of micronutrient intakes.

PMID:35593158 | DOI:10.1080/19485565.2022.2072269

Health Soc Care Community. 2022 May 20. doi: 10.1111/hsc.13842. Online ahead of print.

ABSTRACT

Nordic walking (NW) may be a beneficial treatment for people with Parkinson’s disease (PD). Since high-quality research has been published on the effects of NW on people with PD by now, an actualised and comprehensive, in-depth review is recommended to guide practitioners in prescribing this exercise modality. The purpose of this study was to conduct a systematic review and meta-analysis on the effectiveness of NW as a rehabilitation strategy for PD. According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a literature search was performed using Pubmed, SportDiscus and Scopus up to May 2021. Randomised controlled trials (RCTs) addressing the impact of a NW intervention on any outcomes in people with PD were included. The critical appraisal of the RCTs was retrieved from the Physiotherapy Evidence Database (PEDro) or evaluated using the PEDro scale. The Cochrane Collaboration’s risk of bias tool was also employed. The review was not registered a priori on any database and a review protocol was not published. Twelve studies were included in the review. The investigations were mostly good-to-fair methodological quality, and risk of bias was acceptable. None of the reported statistically significant benefits of NW were clinically meaningful, except for walking ability. Although adherence to NW programs was good, some adverse effects derived from its practice were informed. The practice of Nordic Walking does not lead to clinically significant changes in global motor impairment, functional mobility, balance and physical fitness in patients with PD. This therapy seems to improve walking ability and quality of life, although further research in this latter outcome is needed.

PMID:35593147 | DOI:10.1111/hsc.13842

Phys Chem Chem Phys. 2022 May 20. doi: 10.1039/d2cp01585d. Online ahead of print.

ABSTRACT

Many references exist in the density functional theory (DFT) literature to the chemical potential of the electrons in an atom or a molecule. The origin of this notion has been the identification of the Lagrange multiplier μ = ∂E/∂N in the Euler-Lagrange variational equation for the ground state density as the chemical potential of the electrons. We first discuss why the Lagrange multiplier in this case is an arbitrary constant and therefore cannot be a physical characteristic of an atom or molecule. The switching of the energy derivative (“chemical potential”) from –I to –A when the electron number crosses the integer, called integer discontinuity or derivative discontinuity, is not physical but only occurs when the nonphysical noninteger electron systems and the corresponding energy and derivative ∂E/∂N are chosen in a specific discontinuous way. The question is discussed whether in fact the thermodynamical concept of a chemical potential can be defined for the electrons in such few-electron systems as atoms and molecules. The conclusion is that such systems lack important characteristics of thermodynamic systems and do not afford the definition of a chemical potential. They also cannot be considered as analogues of the open systems of thermodynamics that can exchange particles with an environment (a particle bath or other members of a Gibbsian ensemble). Thermodynamical (statistical mechanical) concepts like chemical potential, open systems, grand canonical ensemble etc. are not applicable to a few electron system like an atom or molecule. A number of topics in DFT are critically reviewed in light of these findings: jumps in the Kohn-Sham potential when crossing an integer number of electrons, the band gap problem, the deviation-from-straight-lines error, and the role of ensembles in DFT.

PMID:35593143 | DOI:10.1039/d2cp01585d